hi, i'd like to do a simulation of a solute in water - trying to reproduce some literature data i try to be consistent and use an atom-based cut-off. for this each atom needs to be its own charge-group ... so when i change spc.itp from: 1 opls_116 1 SOL OW 1 -0.82 2 opls_117 1 SOL HW1 1 0.41 3 opls_117 1 SOL HW2 1 0.41 to: 1 opls_116 1 SOL OW 1 -0.82 2 opls_117 1 SOL HW1 2 0.41 3 opls_117 1 SOL HW2 3 0.41
grompp complains that for settle all atoms need to be in the same charge group. so i removed the settle and exclusion statements from spc.itp and instead put the commands constraints = h-angles constraint_algorithm = LINCS lincs_order = 8 lincs_iter = 2 in the mdp file ... but now constraints are not applied to waters at all (O and H look as if they move independently) it also didn't help renaming the water molecule, residue and atom names ... any suggestions on how i can apply atom-based cut-off with lincs or shake to water? thanks, michael =============================== Why be happy when you could be normal? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
